Small cardamom (Elettaria cardamomum Maton) a perennial monocot, exhibits an array of variation in nature, mainly due to cross pollination. Based on the nature of the panicle orientation, cardamom is broadly grouped into three main ‘cultivated types’ – Malabar, Mysore and Vazhuka having prostrate, erect and semi-erect panicles respectively. These morphologically discriminative markers manifest itself during panicle emergence as is only possible. Among the three varieties Malabar variety is relatively superior with respect to different qualitative and quantitative characteristics. The objective of the present study was to develop and characterize molecular markers for enabling differentiation of Malabar variety at juvenile stage. One accession specific ISSR marker generated by UBC 866 was selected which consistently amplified an intact, distinct, ̴1500bp band specifically in individuals of Malabar variety, which was therefore cloned, sequenced and characterized. Ten primers were designed from the sequences for converting them to SCAR markers. The developed SCAR markers were tested for variety specificity and one primer pair (SBBT4F/SBBT3R) was validated using small cardamom accessions belonging to Malabar variety from different geographic locations and varieties with erect panicles as well as hybrids. The findings suggest that the SCAR marker is promising in identifying cardamom varieties having prostrate panicle (Malabar) and therefore is expected to make significant contributions in selection of F1 hybrids during breeding programmes.